This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Multiscale simulation methods are being created and applied to the study of synaptic activity and the discovery of new pharmaceuticals. For synaptic activity, the simulations include QM/MM studies of acetylcholinesterase (AChE), analysis of the kinetics of AChE and the activity of ACh receptors, and integrated analyses of all of these components in model synapses. These simulations depend on novel theory and software for molecular modeling, including advanced methods for the modeling of electrostatics, diffusion, mechanics, and hydrodynamics at the supramolecular scale. These same methods are used in novel ways to facilitate discovery of drugs for neurological diseases, and for other diseases including HIV/AIDS and cancer.